Installing ez-4.0.0 via github

[John Sheppard]

Dear Mike,

First off, thank you for creating the 'ez' package and making it
available to the community -- it has been extremely helpful and
allowed me to carry out some analyses in R that I'd otherwise have had
to resort to Matlab for.

Recently, I'd been retrieving the latest developer's version of the
package whenever I needed to run ezANOVA(), as I believe there was a
bug that affected performance for completely between-subjects designs
(which affected me but worked fine after getting the latest code) -->
http://groups.google.com/group/ez4r/browse_thread/thread/2273ce7e42f34f83

I noticed that executing this line now gives an error:
> eval(expr = parse(text=getURL('https://raw.github.com/mike-lawrence/ez/master/R/ezDev.R',ssl.verifypeer=FALSE)));
Error in parse(text = getURL("https://raw.github.com/mike-lawrence/ez/
master/R/ezDev.R", :
<text>:1:1: unexpected '<'
1: <
^

However, I then realized today that a new version of the ez package
(4.0.0) has been uploaded to github. Perhaps the latest version now
has fixed the bug involving completely between-Subject designs?

Unfortunately, I got an error when trying to follow the installation
instructions for the newest version on github (https://github.com/mike-
lawrence/ez):

> install_github("ez","mike-lawrence")
Installing ez from mike-lawrence
Installing ez
* checking for file 'C:\Documents and Settings\Administrator\Local
Settings\Temp\RtmpeIVe3q\mike-lawrence-ez-962d338/DESCRIPTION' ... OK
* preparing 'ez':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'ez_4.0-0.tar.gz'
ERROR
packaging into .tar.gz failed
Error: Command failed (1)
In addition: Warning message:
running command '"C:/PROGRA~1/R/R-214~1.0/bin/i386/R" CMD build "C:
\Documents and Settings\Administrator\Local Settings\Temp\RtmpeIVe3q
\mike-lawrence-ez-962d338" --no-manual --no-vignettes' had status 1
>


I am curious if there is an obvious reason for this error message, or
if I may be doing something wrong and/or the problem relates to my
platform (it is 32-bit WinXP running R 2.14.0 on a Virtual Machine
through my Mac)? (Not sure if I have provided enough information --
let me know if not.)

Also, if the automatic install does not work, perhaps I could simply
install the latest updates manually. I did not seem to see a new
package available for manual download. Admittedly, I am a novice in R
(most of my experience is with Matlab) so perhaps this process should
be quite straightforward and I'm missing something obvious.

Anyway, if you and/or anyone else has any advice on getting the latest
version (that isn't afflicted with the between-S design issue), it
would be a great help!

Thanks much,
John S.

[Mike Lawrence]

Hi John,

As I indicate in a note just sent to this list (indeed, your message
reminded me that I should give people a heads up on this), I changed
the instructions on how to install the dev version of ez and
intentionally broke the older method. Unfortunately it seems that on
your set up this causes problems and I'll have to check with a
colleague that uses windows to see if I can track down what's going
on. In the meantime, is there any reason you're running R in a virtual
machine when there is a native OS X version of R?

Finally, if you really want the old way of using the dev version of ez
back, you can download the now deprecated ezDev() function from here:

https://raw.github.com/mike-lawrence/ez/d08fd65f9fda27ff58a35e03f6b2716d7e1011c9/R/ezDev.R

Simply source that and you should be good to go.

Mike

[John Sheppard]

Hi Mike,

Thanks for getting back to me so soon. I had been resorting to the
Windows version of R only because on Mac OSX, R 2.14.0 (and earlier
versions) have been failing when trying to add new packages (e.g. via
install.packages()). I believe this is simply a matter of configuring
the settings for search-able repositories, which apparently does not
work for me out of the box in OSX. Basically I was impatient and found
that Windows R on my virtual machine worked fine for adding packages
without any fuss. It would certainly make things simpler to just do
everything in OSX though, so perhaps I'll work on getting those
repositories properly configured (which I presume is the problem),
especially now that I understand that this problem with github seems
to be related to my OS. In the meantime, though, thanks for letting me
know about the work-around with ezDev().

Best,
John

On Feb 1, 11:56 am, Mike Lawrence <Mike.Lawre...@dal.ca> wrote:
> Hi John,
>
> As I indicate in a note just sent to this list (indeed, your message
> reminded me that I should give people a heads up on this), I changed
> the instructions on how to install the dev version of ez and
> intentionally broke the older method. Unfortunately it seems that on
> your set up this causes problems and I'll have to check with a
> colleague that uses windows to see if I can track down what's going
> on. In the meantime, is there any reason you're running R in a virtual
> machine when there is a native OS X version of R?
>
> Finally, if you really want the old way of using the dev version of ez
> back, you can download the now deprecated ezDev() function from here:
>

> https://raw.github.com/mike-lawrence/ez/d08fd65f9fda27ff58a35e03f6b27...

>
> Simply source that and you should be good to go.
>
> Mike
>

> On Tue, Jan 31, 2012 at 11:44 PM, John Sheppard <jsheppar...@gmail.com> wrote:
> > Dear Mike,
>
> > First off, thank you for creating the 'ez' package and making it
> > available to the community -- it has been extremely helpful and
> > allowed me to carry out some analyses in R that I'd otherwise have had
> > to resort to Matlab for.
>
> > Recently, I'd been retrieving the latest developer's version of the
> > package whenever I needed to run ezANOVA(), as I believe there was a
> > bug that affected performance for completely between-subjects designs
> > (which affected me but worked fine after getting the latest code) -->

> >http://groups.google.com/group/ez4r/browse_thread/thread/2273ce7e42f3...

>
> > I noticed that executing this line now gives an error:

> >> eval(expr = parse(text=getURL('https://raw.github.com/mike-lawrence/ez/master/R/ezDev.R',ssl.verifyp...

[Mike Lawrence]

On Wed, Feb 1, 2012 at 10:51 PM, John Sheppard <jshep...@gmail.com> wrote:
> Thanks for getting back to me so soon. I had been resorting to the
> Windows version of R only because on Mac OSX, R 2.14.0 (and earlier
> versions) have been failing when trying to add new packages (e.g. via
> install.packages()).

Interesting, I've never encountered any problems with R on OS X. Do
you get the same error regardless of whether you run R from the GUI vs
from within terminal.app?

[John Sheppard]

Hey Mike,

Well, it looks like you just solved my Mac OSX R problems!

In terminal:

> install.packages("devtools")

--- Please select a CRAN mirror for use in this session ---

Loading Tcl/Tk interface ... done

CRAN mirror 

 1: Argentina (La Plata)      2: Argentina (Mendoza)    

 3: Australia (Canberra)      4: Australia (Melbourne)  

 5: Austria                   6: Belgium                

 7: Brazil (PR)               8: Brazil (RJ)            

 9: Brazil (SP 1)            10: Brazil (SP 2)          

11: Canada (BC)              12: C

etc etc etc.....

The downloaded packages are in

/var/folders/PI/PI-MlWxZFFW1Ffj3eQGnf++++TI/-Tmp-//RtmpceSO3b/downloaded_packages

> 

In R GUI:

> install.packages("devtools")

Warning: unable to access index for repository http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/leopard/contrib/2.14

Warning message:

In getDependencies(pkgs, dependencies, available, lib) :

  package ‘devtools’ is not available (for R version 2.14.1)

> 

Funny that I didn't even try terminal to see if there was a difference.. used to use terminal for R all the time back when I ran Ubuntu - guess I don't quite understand why there should be a difference, but anyway, this would seem to solve my problems as I have no preference for running in GUI over terminal.

(Both terminal & gui are R 2.14.1 for x64.. GUI still fails with basic R instead of R64.)

Thanks!

John

[Mike Lawrence]

I suspect that the problem was simply at the install stage, and now
that you have devtools installed you can use the GUI.

With respect to why the GUI failed in the first place, I wonder if you
have a default repository mirror set in your GUI preferences that is
different from the GUI chosen when you ran R in the terminal? In this
case, I would suspect that the mirror you were using in the GUI isn't
well maintained and therefore didn't have the latest devtools for R
14.1

[Sawfoot]

I have the same problem  on windows, most recent version of R.

of note is that when run devtools I got his message.

> library(devtools)
Rtools not installed.

> install.packages("Rtools")
Installing package(s) into ‘C:/Documents and Settings/sawfoot/My Documents/R-dev’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘Rtools’ is not available (for R version 2.14.1)

[Mike Lawrence]

I think you have to install RTools from the exe available here:

http://cran.r-project.org/bin/windows/Rtools/

[Shane Lindsay]

That worked (once I updated a bunch of packages).

Thanks

[Robert Day]

Hi Mike,

I too am very new to R, having used Systat previously.

I am trying to install ez on a Mac OS X El Capitan (10.11.6).

I found I needed to change the install.packages to have "devtools" not ''.

But when I tried to install on github, everything went ok until:

* installing *source* package ‘ez’ ...

** R

** data

** byte-compile and prepare package for lazy loading

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 

  there is no package called ‘pbkrtest’

ERROR: lazy loading failed for package ‘ez’

* removing ‘/Users/admin/R-dev/ez’

Error: Command failed (1)

I also tried the code you sent to John Shepherd, but after implementing it, I could not find package ez in the search area.

Perhaps I am missing something there?

Thanks for your help, Rob

[Mike Lawrence]

Strange. Doing the following works fine for me::

    install.packages('devtools')

    library('devtools')

    devtools::install_github('mike-lawrence/ez')

--
Mike Lawrence
Graduate Student
Department of Psychology & Neuroscience
Dalhousie University

~ Certainty is (possibly) folly ~